SBS Mutational Signatures Analysis

Purpose:

Calculate and plot mutational signatures for all samples using COSMIC signatures and Alexandrov et al, 2013 mutational signatures.

Usage

To run this from the command line, use: Rscript -e "rmarkdown::render('analyses/mutational-signatures/01-known_signatures.Rmd', clean = TRUE)"

This assumes you are in the top directory of the repository.

Setup

Packages and functions

Import necessary functions.

# Magrittr pipe
`%>%` <- dplyr::`%>%`

# Import specialized functions
source(file.path("util", "mut_sig_functions.R"))

# Load this library
library(deconstructSigs)
library(tidyverse)

── Attaching core tidyverse packages ────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.1     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.2     ✔ tibble    3.2.1
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.1     
── Conflicts ──────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

library("optparse")

set options

snv_file <- params$snv_file
output_Folder <- params$output_Folder

Set up directory paths.

data_dir <- file.path("..", "..", "data")
input_dir <- "input"
results_dir <- file.path("results", output_Folder)
plots_dir <- file.path("plots", output_Folder)
figures_dir <- file.path("..", "..", "figures")

cosmicv2_plots <- file.path(plots_dir, "cosmicv2")
nature_plots <- file.path(plots_dir, "nature")
cosmicv3_plots <- file.path(plots_dir, "cosmicv3")

scratch_dir <- file.path("..", "..", "scratch", "mutational-signatures")
cosmicv2_scratch <- file.path(scratch_dir, output_Folder, "cosmicv2")
cosmicv3_scratch <- file.path(scratch_dir, output_Folder, "cosmicv3")
nature_scratch <- file.path(scratch_dir, output_Folder, "nature")

Make new directories for the results.

if (!dir.exists(results_dir)) {
  dir.create(results_dir)
}
if (!dir.exists(cosmicv2_plots)) {
  dir.create(cosmicv2_plots, recursive = TRUE)
}
if (!dir.exists(nature_plots)) {
  dir.create(nature_plots, recursive = TRUE)
}
if (!dir.exists(cosmicv3_plots)) {
  dir.create(cosmicv3_plots, recursive = TRUE)
}

if (!dir.exists(scratch_dir)) {
  dir.create(scratch_dir)
}
if (!dir.exists(cosmicv2_scratch)) {
  dir.create(cosmicv2_scratch)
}
if (!dir.exists(cosmicv3_scratch)) {
  dir.create(cosmicv3_scratch)
}
if (!dir.exists(nature_scratch)) {
  dir.create(nature_scratch)
}

Read in data

# Declare file path for consensus file
consensus_file <- file.path(data_dir, snv_file)

Read in the consensus MAF file.

# Read in the file
maf <- data.table::fread(consensus_file, data.table = FALSE)

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Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

Warning in writeBin(bfr, con = out, size = 1L): problem writing to connection

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Warning in data.table::fread(consensus_file, data.table = FALSE): Discarded
single-line footer: <<PURPL 0 . GR>>

Read in color palettes

Read in the histology colors and labels.

histology_label_mapping <- readr::read_tsv(
  file.path(figures_dir, "palettes", "histology_label_color_table.tsv")
) %>% 
  # Select just the columns we will need for plotting
  dplyr::select(Kids_First_Biospecimen_ID, display_group, display_order, hex_codes) %>% 
  # Reorder display_group based on display_order
  dplyr::mutate(display_group = forcats::fct_reorder(display_group, display_order))

Rows: 2840 Columns: 15
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (11): Kids_First_Biospecimen_ID, sample_type, integrated_diagnosis, Note...
dbl  (4): n, display_order, cancer_group_n, cancer_group_order

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Set up gradient color palette for the bubble matrix plots.

gradient_col_palette <- readr::read_tsv(
  file.path(figures_dir, "palettes", "gradient_color_palette.tsv")
)

Rows: 11 Columns: 2
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): color_names, hex_codes

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# Won't need NA color this time. 
gradient_col_palette <- gradient_col_palette %>%
  dplyr::filter(color_names != "na_color")

Read in the metadata and set it up with the color palette. Separate BS_ids into intial CNS tumors and other tumors, as mutational signatures analyses will be run on a different set of signatures for each group.

metadata_df <- readr::read_tsv(file.path(data_dir, "histologies.tsv"), guess_max = 10000) %>% 
#  dplyr::select("Kids_First_Biospecimen_ID", "experimental_strategy") %>%
  dplyr::inner_join(histology_label_mapping, by = "Kids_First_Biospecimen_ID") %>% 
  dplyr::rename(Tumor_Sample_Barcode = "Kids_First_Biospecimen_ID") 

Rows: 47507 Columns: 58
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
dbl (17): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

initial_pretx_tumors <- metadata_df %>%
  filter(tumor_descriptor == "Initial CNS Tumor" & age_at_diagnosis_days < age_at_chemo_start) %>%
  pull(Tumor_Sample_Barcode)

Read in tmb-all file with WGS and WXS region lengths so they can be used for the Mb denominator.

# Set up BED region file for TMB calculations
region_sizes <- readr::read_tsv(file.path(data_dir, "snv-mutation-tmb-all.tsv")) %>%
  dplyr::select(Tumor_Sample_Barcode, region_size)

Rows: 4148 Columns: 5
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): Tumor_Sample_Barcode, experimental_strategy
dbl (3): mutation_count, region_size, tmb

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Set up data

Determine how many mutations we have per sample.

mut_per_sample <- maf %>%
  dplyr::group_by(Tumor_Sample_Barcode) %>%
  dplyr::tally() %>%
  dplyr::arrange(n)

summary(mut_per_sample$n)

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
     8.0    146.8   1625.5   2912.3   2881.8 171779.0 

Graph this.

ggplot2::ggplot(mut_per_sample, ggplot2::aes(x = n, geom = "density")) +
  ggplot2::geom_density() +
  ggplot2::theme_classic()

Make mutation data into deconstructSigs input format.

# Convert to deconstructSigs input
sigs_input <- mut.to.sigs.input(
  mut.ref = maf,
  sample.id = "Tumor_Sample_Barcode",
  chr = "Chromosome",
  pos = "Start_Position",
  ref = "Reference_Allele",
  alt = "Allele",
  bsg = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
)

Warning in mut.to.sigs.input(mut.ref = maf, sample.id = "Tumor_Sample_Barcode", : Some samples have fewer than 50 mutations:
  BS_7KR13R3P, BS_Z8GRJ71M, BS_YGDHJ68W, BS_X0KN4VVW, BS_W60PB1DS, BS_ST7KGV85, BS_QF7M4SHH, BS_P7VR731D, BS_KT3GAAQV, BS_KHJMCFQR, BS_GQFPB8F3, BS_GJ2KS7BT, BS_BTDQZ60Q, BS_91HP99HY, BS_4SCDT7M9, BS_3DV5FVPQ, BS_1B00Q25Y, BS_02QV7ZWP

Add total mutations per sample.

# Count the total number of signature mutations for each sample
total_muts <- apply(sigs_input, 1, sum)

Determine Signatures for COSMIC and Alexandrov et al, 2013

Get list of tumor sample ids.

tumor_sample_ids <- maf %>%
  dplyr::filter(Tumor_Sample_Barcode %in% rownames(sigs_input)) %>%
  dplyr::distinct(Tumor_Sample_Barcode) %>%
  dplyr::pull(Tumor_Sample_Barcode)

Get COSMIC v2 signatures for each sample. This step will take some time.

sample_sigs_cosmic <- lapply(tumor_sample_ids, function(sample_id) {
  # Determine the signatures contributing to the sample
  whichSignatures(
    tumor.ref = sigs_input,
    signatures.ref = signatures.cosmic,
    sample.id = sample_id,
    contexts.needed = TRUE
  )
})
# Bring along the names
names(sample_sigs_cosmic) <- tumor_sample_ids

# Create matrix of COSMIC signature weights
cosmic_weights <- lapply(sample_sigs_cosmic, "[[", "weights")
cosmic_wide <- do.call(dplyr::bind_rows, cosmic_weights) %>%
  add_column('Kids_First_Biospecimen_ID' = unlist(lapply(cosmic_weights, rownames)), .before = 1) %>%
  tibble::as_tibble() %>%
readr::write_tsv(file.path(results_dir, 'cosmicv2_signature_exposure_matrix.tsv'))

Get Alexandrov et al, 2013 signatures for each sample.

sample_sigs_nature <- lapply(tumor_sample_ids, function(sample_id) {
  # Determine the signatures contributing to the sample
  whichSignatures(
    tumor.ref = sigs_input,
    signatures.ref = signatures.nature2013,
    sample.id = sample_id,
    contexts.needed = TRUE
  )
})
# Bring along the names
names(sample_sigs_nature) <- tumor_sample_ids

# Create data frame of Nature signature weights
nature_weights <- lapply(sample_sigs_nature, "[[", "weights")
nature_wide <- do.call(dplyr::bind_rows, nature_weights) %>%
  add_column('Kids_First_Biospecimen_ID' = unlist(lapply(nature_weights, rownames)), .before = 1) %>%
  tibble::as_tibble() %>%
readr::write_tsv(file.path(results_dir, 'nature_signature_exposure_matrix.tsv'))

Get COSMIC genome v3.3 signatures for each sample.

signatures.cosmic.v3.3 <- read_tsv(file.path(input_dir, 'COSMIC_v3.3.1_SBS_GRCh38.txt')) %>%
  column_to_rownames('Type') %>%
  t %>%
  as.data.frame()

Rows: 96 Columns: 80
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr  (1): Type
dbl (79): SBS1, SBS2, SBS3, SBS4, SBS5, SBS6, SBS7a, SBS7b, SBS7c, SBS7d, SB...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Create list of include/exclude signatures using SBSv3 mapping file. For Initial CNS tumors, therapy exposures will be excluded, but they will be retained for other tumor types.

map <- read_tsv(file.path(input_dir, "sbs_v3_map.tsv"))

Rows: 79 Columns: 4
── Column specification ──────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): Signature, Meaning, Broad_category, Narrow_category

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# Excluded signatures:
artifact_sigs <- map %>%
   filter(Broad_category == "Sequencing artifact") %>%
   pull(Signature)

environ_sigs <- map %>%
   filter(Broad_category == "Environmental exposure") %>%
   pull(Signature)

unknown <- map %>%
   filter(Broad_category == "Unknown" & Signature != "SBS39") %>%
   pull(Signature)
 
therapy_sigs <- map %>%
   filter(Broad_category == "Therapy exposure") %>%
   pull(Signature)

exclude_sigs <- c(artifact_sigs, environ_sigs, unknown)
include_sigs_initialPretx <- setdiff(rownames(signatures.cosmic.v3.3), c(exclude_sigs, therapy_sigs))
include_sigs_other <- setdiff(rownames(signatures.cosmic.v3.3), exclude_sigs)

Run signature extraction. This step will take some time.

sample_sigs_cosmic_v33 <- lapply(tumor_sample_ids, function(sample_id) {
  # Determine the signatures contributing to the sample
  if (sample_id %in% initial_pretx_tumors){
    whichSignatures(
    tumor.ref = sigs_input,
    signatures.ref = signatures.cosmic.v3.3,
    sample.id = sample_id,
    contexts.needed = TRUE,
    associated = include_sigs_initialPretx
    )
  }else{
    whichSignatures(
    tumor.ref = sigs_input,
    signatures.ref = signatures.cosmic.v3.3,
    sample.id = sample_id,
    contexts.needed = TRUE,
    associated = include_sigs_other
    )
  }
})

# Bring along the names
names(sample_sigs_cosmic_v33) <- tumor_sample_ids
# 
# Create matrix of COSMIC signature weights
cosmic_v33_weights <- lapply(sample_sigs_cosmic_v33, "[[", "weights")
cosmic_v33_wide <- do.call(dplyr::bind_rows, cosmic_v33_weights) %>%
  add_column('Kids_First_Biospecimen_ID' = unlist(lapply(cosmic_v33_weights, rownames)), .before = 1) %>%
  tibble::as_tibble() %>%
  readr::write_tsv(file.path(results_dir, 'cosmicv3.3_signature_exposure_matrix.tsv'))

Calculate the mutations per Mb for each signature

Do this for COSMIC v2 mutation signatures.

# Calculate mutations per signature
cosmic_sigs_df <- calc_mut_per_sig(
  sample_sigs_cosmic,
  muts_per_sample = total_muts,
  region_size = region_sizes,
  metadata = metadata_df
)  %>%
  dplyr::filter(grepl("Signature", signature))

Using Tumor_Sample_Barcode, Kids_First_Participant_ID, sample_id, aliquot_id, sample_type, tumor_descriptor, composition, cell_line_composition, pathology_diagnosis, pathology_free_text_diagnosis, cancer_predispositions, cohort, sub_cohort, experimental_strategy, RNA_library, match_id, cohort_participant_id, primary_site, CNS_region, reported_gender, germline_sex_estimate, race, ethnicity, OS_status, EFS_event_type, extent_of_tumor_resection, clinical_status_at_event, seq_center, broad_histology, short_histology, molecular_subtype, molecular_subtype_methyl, cancer_group, integrated_diagnosis, harmonized_diagnosis, Notes, dkfz_v12_methylation_subclass, dkfz_v12_methylation_mgmt_status, dkfz_v11_methylation_subclass, gtex_group, gtex_subgroup, display_group, hex_codes as id variables

Warning: attributes are not identical across measure variables; they will be
dropped

# Write this to a file but drop the color column
cosmic_sigs_df %>% 
  dplyr::select(-hex_codes) %>% 
  readr::write_tsv(file.path(results_dir, "cosmicv2_signatures_results.tsv"))

# Print out a preview
cosmic_sigs_df

Do this for COSMIC v3.3 mutation signatures.

# Calculate mutations per signature
cosmicv3_sigs_df <- calc_mut_per_sig(
  sample_sigs_cosmic_v33,
  muts_per_sample = total_muts,
  region_size = region_sizes,
  metadata = metadata_df
) %>%
  dplyr::filter(grepl("SBS", signature))

Using Tumor_Sample_Barcode, Kids_First_Participant_ID, sample_id, aliquot_id, sample_type, tumor_descriptor, composition, cell_line_composition, pathology_diagnosis, pathology_free_text_diagnosis, cancer_predispositions, cohort, sub_cohort, experimental_strategy, RNA_library, match_id, cohort_participant_id, primary_site, CNS_region, reported_gender, germline_sex_estimate, race, ethnicity, OS_status, EFS_event_type, extent_of_tumor_resection, clinical_status_at_event, seq_center, broad_histology, short_histology, molecular_subtype, molecular_subtype_methyl, cancer_group, integrated_diagnosis, harmonized_diagnosis, Notes, dkfz_v12_methylation_subclass, dkfz_v12_methylation_mgmt_status, dkfz_v11_methylation_subclass, gtex_group, gtex_subgroup, display_group, hex_codes as id variables

Warning: attributes are not identical across measure variables; they will be
dropped

# Write this to a file but drop the color column
cosmicv3_sigs_df %>% 
#  dplyr::filter(grepl("SBS", signature)) %>%
  dplyr::select(-hex_codes) %>% 
  readr::write_tsv(file.path(results_dir, "cosmicv3.3_signatures_results.tsv"))

# Print out a preview
cosmicv3_sigs_df

Do this for Alexandrov et al, 2013 mutation signatures.

#Calculate mutations per signature
nature_sigs_df <- calc_mut_per_sig(
  sample_sigs_nature,
  muts_per_sample = total_muts,
  region_size = region_sizes,
  metadata = metadata_df
)  %>%
  dplyr::filter(grepl("Signature", signature))

Using Tumor_Sample_Barcode, Kids_First_Participant_ID, sample_id, aliquot_id, sample_type, tumor_descriptor, composition, cell_line_composition, pathology_diagnosis, pathology_free_text_diagnosis, cancer_predispositions, cohort, sub_cohort, experimental_strategy, RNA_library, match_id, cohort_participant_id, primary_site, CNS_region, reported_gender, germline_sex_estimate, race, ethnicity, OS_status, EFS_event_type, extent_of_tumor_resection, clinical_status_at_event, seq_center, broad_histology, short_histology, molecular_subtype, molecular_subtype_methyl, cancer_group, integrated_diagnosis, harmonized_diagnosis, Notes, dkfz_v12_methylation_subclass, dkfz_v12_methylation_mgmt_status, dkfz_v11_methylation_subclass, gtex_group, gtex_subgroup, display_group, hex_codes as id variables

Warning: attributes are not identical across measure variables; they will be
dropped

# Write this to a file but drop the color column
nature_sigs_df %>% 
#  dplyr::filter(grepl("SBS", signature)) %>%
  dplyr::select(-hex_codes) %>% 
  readr::write_tsv(file.path(results_dir, "nature_signatures_results.tsv"))

# Print out a preview
nature_sigs_df

Mutation signature bubble matrix by histology groups

For COSMIC v2 signatures

bubble_matrix_plot(cosmic_sigs_df, 
                   label = "COSMIC Signatures", 
                   color_palette = gradient_col_palette$hex_codes
)

`summarise()` has grouped output by 'display_group'. You can override using the
`.groups` argument.

Warning: Removed 335 rows containing missing values (`geom_point()`).

ggplot2::ggsave(
  file.path(cosmicv2_plots, "bubble_matrix_cosmicv2_mutation_sig.png"),
  width = 30, height = 20, units = "cm")

Warning: Removed 335 rows containing missing values (`geom_point()`).

For Nature signatures

bubble_matrix_plot(nature_sigs_df, 
                   label = "Alexandrov et al, 2013 signatures", 
                   color_palette = gradient_col_palette$hex_codes)

`summarise()` has grouped output by 'display_group'. You can override using the
`.groups` argument.

Warning: Removed 281 rows containing missing values (`geom_point()`).

ggplot2::ggsave(
  file.path(nature_plots, "bubble_matrix_nature_mutation_sig.png"), 
  width = 30, height = 20, units = "cm")

Warning: Removed 281 rows containing missing values (`geom_point()`).

For COSMIC v3.3 signatures

bubble_matrix_plot(cosmicv3_sigs_df, 
                   label = "COSMIC Signatures", 
                   color_palette = gradient_col_palette$hex_codes
)

`summarise()` has grouped output by 'display_group'. You can override using the
`.groups` argument.

Warning: Removed 1116 rows containing missing values (`geom_point()`).

ggplot2::ggsave(
  file.path(cosmicv3_plots, "bubble_matrix_cosmicv3_mutation_sig.png"),
  width = 30, height = 20, units = "cm")

Warning: Removed 1116 rows containing missing values (`geom_point()`).

Mutation signature grouped bar plots for each histology group

We will make these plots for primary tumor samples only. Lets make these for COSMIC mutation signatures first.

# Make grouped bar plots
lapply(unique(cosmic_sigs_df$display_group),
  grouped_sig_barplot,
  sig_num_df = cosmic_sigs_df,
  output_dir = file.path(cosmicv2_scratch, "signature_grouped_barplots"), 
  label = "cosmic_v2"
)

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Make these plots for Alexandrov et al, 2013 signatures.

# Make grouped bar plots
lapply(unique(nature_sigs_df$display_group),
  grouped_sig_barplot,
  sig_num_df = nature_sigs_df,
  output_dir = file.path(nature_scratch, "signature_grouped_barplots"),
  label = "nature"
)

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Make these plots for COSMIC v3.3 signatures.

# Make grouped bar plots
lapply(unique(cosmicv3_sigs_df$display_group),
  grouped_sig_barplot,
  sig_num_df = cosmicv3_sigs_df,
  output_dir = file.path(cosmicv3_scratch, "signature_grouped_barplots"),
  label = "cosmic_v3.3"
)

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Session Info

sessionInfo()

R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] optparse_1.7.3        lubridate_1.9.2       forcats_1.0.0        
 [4] stringr_1.5.0         dplyr_1.1.1           purrr_1.0.1          
 [7] readr_2.1.4           tidyr_1.3.0           tibble_3.2.1         
[10] ggplot2_3.4.2         tidyverse_2.0.0       deconstructSigs_1.9.0

loaded via a namespace (and not attached):
 [1] Biobase_2.58.0                    MatrixGenerics_1.10.0            
 [3] sass_0.4.5                        bit64_4.0.5                      
 [5] vroom_1.6.1                       jsonlite_1.8.4                   
 [7] R.utils_2.12.2                    bslib_0.4.2                      
 [9] highr_0.10                        stats4_4.2.3                     
[11] BSgenome_1.66.3                   GenomeInfoDbData_1.2.9           
[13] Rsamtools_2.14.0                  yaml_2.3.7                       
[15] lattice_0.21-8                    pillar_1.9.0                     
[17] glue_1.6.2                        digest_0.6.31                    
[19] GenomicRanges_1.50.2              XVector_0.38.0                   
[21] colorspace_2.1-0                  plyr_1.8.8                       
[23] Matrix_1.5-4                      htmltools_0.5.5                  
[25] R.oo_1.25.0                       XML_3.99-0.14                    
[27] pkgconfig_2.0.3                   zlibbioc_1.44.0                  
[29] scales_1.2.1                      getopt_1.20.3                    
[31] tzdb_0.3.0                        BiocParallel_1.32.6              
[33] timechange_0.2.0                  generics_0.1.3                   
[35] farver_2.1.1                      IRanges_2.32.0                   
[37] SummarizedExperiment_1.28.0       cachem_1.0.7                     
[39] withr_2.5.0                       BiocGenerics_0.44.0              
[41] cli_3.6.1                         magrittr_2.0.3                   
[43] crayon_1.5.2                      evaluate_0.20                    
[45] R.methodsS3_1.8.2                 fansi_1.0.4                      
[47] textshaping_0.3.6                 tools_4.2.3                      
[49] data.table_1.14.8                 hms_1.1.3                        
[51] BiocIO_1.8.0                      lifecycle_1.0.3                  
[53] matrixStats_0.63.0                S4Vectors_0.36.2                 
[55] munsell_0.5.0                     DelayedArray_0.24.0              
[57] Biostrings_2.66.0                 compiler_4.2.3                   
[59] jquerylib_0.1.4                   GenomeInfoDb_1.34.9              
[61] systemfonts_1.0.4                 rlang_1.1.0                      
[63] grid_4.2.3                        RCurl_1.98-1.12                  
[65] rjson_0.2.21                      bitops_1.0-7                     
[67] labeling_0.4.2                    rmarkdown_2.21                   
[69] restfulr_0.0.15                   gtable_0.3.3                     
[71] codetools_0.2-19                  reshape2_1.4.4                   
[73] R6_2.5.1                          GenomicAlignments_1.34.1         
[75] knitr_1.42                        rtracklayer_1.58.0               
[77] fastmap_1.1.1                     bit_4.0.5                        
[79] utf8_1.2.3                        ragg_1.2.5                       
[81] stringi_1.7.12                    Rcpp_1.0.10                      
[83] parallel_4.2.3                    vctrs_0.6.2                      
[85] tidyselect_1.2.0                  xfun_0.38                        
[87] BSgenome.Hsapiens.UCSC.hg38_1.4.5